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RFLPs became the molecular markers of choice for some time due to their
codominance and locus specifi city (Qi et al. 2007 ). Wheat RFLPs were used to
develop high-resolution genetic and physical maps (Qi et al. 2004 ; Qi et al. 2003 ),
characterize homoeology of alien chromosome s, and reveal their rearrangements
relative to wheat (Devos et al. 1993 ; Devos and Gale 1993 ; Zhang et al. 1998 ;
McArthur et al. 2012 ). RFLP markers identifi ed cryptic alien introgressions where
cytogenetic techniques failed (Yingshan et al. 2004 ), such as the T5DL.5DS- 5MgS
wheat- Ae. geniculata translocation conferring resistance to leaf rust and stripe rust
(Kuraparthy et al. 2007 ). With the advances in molecular biology, informative but
cumbersome to use RFLP markers were converted to PCR-based markers such as
the sequence- tagged site (STS) markers, which were more suitable for tagging
interesting genes (Cenci et al. 1999 ; Seyfarth et al. 1999 ; Langridge et al. 2001 ).
Transposable elements, randomly distributed in nuclear genomes have also been
used as molecular markers (Queen et al. 2003 ; Nagy and Lelley 2003 ). The
sequence-specifi c amplifi ed polymorphism (S-SAP) technology (Waugh et al.
1997 ) amplifi es regions representing fl anking genomic sequences of individual ret-
rotransposons. The advantages of S-SAP for studying genetic diversity are higher
amount of accessible polymorphism (Waugh et al. 1997 ), the markers are more
evenly distributed throughout the genome (Nagy and Lelley 2003 ), and the esti-
mated genetic distances are more consistent with physical mapping (Ellis et al.
1998 ). Nagy et al. ( 2006 ) used the short interspersed nuclear element (SINE) Au
identifi ed in Ae. umbellulata (Yasui et al. 2001 ) to develop S-SAP markers specifi c
for U- and M-genome chromosomes of Aegilops (Nagy et al. 2006 ).
Simple Sequence Repeat (SSR) markers (Tautz 1989 ), or microsatellite markers,
were the next generation of molecular markers employed in wheat–alien introgres-
sion breeding (Mohan et al. 2007 ; Bandopadhyay et al. 2004 ; Yu et al. 2004 ; Gupta
et al. 2003 ). Effi cient development of SSRs requires genomic sequence information,
and thus they were developed concomitantly with expressed sequence tags (ESTs),
cDNA and BAC libraries. A list of genomic resources currently available for
Triticeae is given in Table 13.1.
Together with cDNA libraries and draft genome sequences of barley, bread
wheat, Ae. tauschii and T. urartu (Table 13.2 ), ESTs are currently the most abundant
type of sequence information available for not less than 25 species from 15 Triticeae
genera. The release of 16,000 EST loci mapped to chromosome deletion bins (Qi
et al. 2004 ) provided excellent resource for development of markers from specifi c
chromosome regions and helped designing locus-specifi c markers. Because of the
genic and thus conserved nature of ESTs, EST-derived SSR markers are transfer-
able between Triticeae species (Gupta et al. 2008 ). As ESTs and cDNA resources
are much less abundant in other Triticeae, e.g., Elymus , Aegilops and Leymus,
numerous studies profi ted from the high transferability of wheat EST-derived SSR
markers across distantly related species for comparative mapping, trait-marker
associations and to carry out evolutionary studies to establish the phylogenetic rela-
tionships among the wild relatives of wheat and between them and bread wheat
(Adonina et al. 2005 ; Jing et al. 2007 ; Kroupin et al. 2012 ).
The conserved orthologous set (COS) markers allowed identifi cation of ortholo-
gous regions between wild species and wheat in order to facilitate alien gene- transfer
E. Rey et al.